@datagrok/sequence-translator 1.4.8 → 1.5.0

package/files/polytool-rules/rules_example.json

@@ -1,44 +1,41 @@
-[
-  {
-    "type": "link",
-    "code": "1",
-    "monomericSubstitution": {
-      "firstMonomer": "C",
-      "secondMonomer": "C",
-      "firstLinkingGroup": "3",
-      "secondLinkingGroup": "3",
-      "firstSubstitution": "C",
-      "secondSubstitution": "C"
-    }
-  },
-  {
-    "type": "link",
-    "code": "2",
-    "monomericSubstitution": {
-      "firstMonomer": "NH2",
-      "secondMonomer": "D",
+{
+  "homodimerCode": "#2",
+  "heterodimerCode": "$2",
+  "linkRules": [
+    {
+      "firstMonomers": [
+        "NH2"
+      ],
+      "secondMonomers": [
+        "D"
+      ],
       "firstLinkingGroup": "2",
       "secondLinkingGroup": "3",
-      "firstSubstitution": "NH2",
-      "secondSubstitution": "D"
+      "code": "2"
+    },
+    {
+      "firstMonomers": [
+        "C"
+      ],
+      "secondMonomers": [
+        "C"
+      ],
+      "firstLinkingGroup": "3",
+      "secondLinkingGroup": "3",
+      "code": "1"
     }
-  },
-  {
-    "type": "reaction",
-    "code": "4",
-    "monomericSubstitution": {
-      "firstMonomer": "azG",
-      "secondMonomer": "aG",
+  ],
+  "reactionRules": [
+    {
+      "code": 4,
+      "firstMonomers": [
+        "azG"
+      ],
+      "secondMonomers": [
+        "aG"
+      ],
       "reaction": "[C:1]N=[N+]=[N-].[C:2]C#C>>[C:1]N1-N=NC=C1[C:2]",
       "name": "GGaz"
     }
-  },
-  {
-    "type": "fragmentDuplication",
-    "code": "#3"
-  },
-  {
-    "type": "differentFragments",
-    "code": "$3"
-  }
-]
+  ]
+}

package/package.json

@@ -1,10 +1,10 @@
 {
   "name": "@datagrok/sequence-translator",
   "friendlyName": "Sequence Translator",
-  "version": "1.4.8",
+  "version": "1.5.0",
   "author": {
-    "name": "Alexey Chopovsky",
-    "email": "achopovsky@datagrok.ai"
+    "name": "Leonid Stolbov",
+    "email": "lstolbov@datagrok.ai"
   },
   "description": "SequenceTranslator translates [oligonucleotide](https://en.wikipedia.org/wiki/Oligonucleotide) sequences between [different representations](https://github.com/datagrok-ai/public/tree/master/packages/SequenceTranslator#sequence-representations).",
   "repository": {
@@ -22,10 +22,10 @@
     }
   ],
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.45.5",
+    "@datagrok-libraries/bio": "^5.45.6",
     "@datagrok-libraries/chem-meta": "^1.2.7",
     "@datagrok-libraries/tutorials": "^1.4.3",
-    "@datagrok-libraries/utils": "^4.3.6",
+    "@datagrok-libraries/utils": "^4.3.7",
     "@types/react": "^18.0.15",
     "cash-dom": "^8.1.0",
     "datagrok-api": "^1.21.1",
@@ -39,10 +39,10 @@
     "wu": "^2.1.0"
   },
   "devDependencies": {
-    "@datagrok-libraries/helm-web-editor": "^1.1.12",
-    "@datagrok-libraries/js-draw-lite": "^0.0.9",
-    "@datagrok/bio": "^2.16.6",
-    "@datagrok/helm": "^2.5.7",
+    "@datagrok-libraries/helm-web-editor": "^1.1.13",
+    "@datagrok-libraries/js-draw-lite": "^0.0.10",
+    "@datagrok/bio": "^2.16.8",
+    "@datagrok/helm": "^2.5.8",
     "@datagrok/chem": "^1.12.4",
     "@types/jquery": "^3.5.14",
     "@types/js-yaml": "^4.0.5",

package/src/apps/common/model/oligo-toolkit-package.ts

@@ -5,6 +5,8 @@ import * as DG from 'datagrok-api/dg';
 import {getMonomerLibHelper, IMonomerLibHelper} from '@datagrok-libraries/bio/src/monomer-works/monomer-utils';
 import {IMonomerLib, Monomer} from '@datagrok-libraries/bio/src/types';
 import {LoggerWrapper} from '@datagrok-libraries/bio/src/utils/logger';
+import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
+import {IHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 
 import {APP_NAME} from '../view/const';
 import {DEFAULT_LIB_FILENAME, FALLBACK_LIB_PATH} from './data-loader/const';
@@ -16,14 +18,18 @@ import {MonomerLibWrapper} from './monomer-lib/lib-wrapper';
 import {FormatConverter} from '../../translator/model/format-converter';
 import {FormatDetector} from './parsing-validation/format-detector';
 import {highlightInvalidSubsequence} from '../view/components/colored-input/input-painters';
-import {ISeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 
 export class OligoToolkitPackage extends DG.Package implements ITranslationHelper {
-  private _seqHelper: ISeqHelper;
+
+  private _helmHelper: IHelmHelper;
+  public get helmHelper(): IHelmHelper {
+    if (!this._helmHelper)
+      throw new Error('Package SequenceTranslator .helmHelper is not initialized');
+    return this._helmHelper;
+  }
+
   public get seqHelper(): ISeqHelper {
-    if (!this._seqHelper)
-      throw new Error('Package SequenceTranslator .seqHelper is not initialized');
-    return this._seqHelper;
+    return this._helmHelper.seqHelper;
   }
 
   private _monomerLib?: IMonomerLib;
@@ -60,8 +66,8 @@ export class OligoToolkitPackage extends DG.Package implements ITranslationHelpe
     this._initPromise = initPromise;
   }
 
-  completeInit(seqHelper: ISeqHelper): void {
-    this._seqHelper = seqHelper;
+  completeInit(helmHelper: IHelmHelper): void {
+    this._helmHelper = helmHelper;
   }
 
   private initLibDataPromise?: Promise<void>;

package/src/package.ts

@@ -18,7 +18,7 @@ import {defaultErrorHandler} from './utils/err-info';
 //polytool specific
 import {polyToolConvert, polyToolConvertUI} from './polytool/pt-dialog';
 import {polyToolEnumerateChemUI} from './polytool/pt-dialog';
-import {polyToolEnumerateHelmUI} from './polytool/pt-enumeration-helm-dialog';
+import {polyToolEnumerateHelmUI} from './polytool/pt-enumerate-seq-dialog';
 import {_setPeptideColumn} from './polytool/utils';
 import {PolyToolCsvLibHandler} from './polytool/csv-to-json-monomer-lib-converter';
 import {ITranslationHelper} from './types';
@@ -27,6 +27,7 @@ import {PolyToolConvertFuncEditor} from './polytool/pt-convert-editor';
 import {CyclizedNotationProvider} from './utils/cyclized';
 import {getSeqHelper} from '@datagrok-libraries/bio/src/utils/seq-helper';
 import {PolyToolTags} from './consts';
+import {getHelmHelper} from '@datagrok-libraries/bio/src/helm/helm-helper';
 
 export const _package: OligoToolkitPackage = new OligoToolkitPackage({debug: true}/**/);
 
@@ -34,17 +35,17 @@ let initSequenceTranslatorPromise: Promise<void> | null = null;
 
 //tags: init
 export async function init(): Promise<void> {
-  if (initSequenceTranslatorPromise === null) {
+  if (initSequenceTranslatorPromise === null)
     _package.startInit(initSequenceTranslatorPromise = initSequenceTranslatorInt());
-  }
+
   return initSequenceTranslatorPromise;
 }
 
 async function initSequenceTranslatorInt(): Promise<void> {
-  const [seqHelper] = await Promise.all([
-    getSeqHelper(),
+  const [helmHelper] = await Promise.all([
+    getHelmHelper(),
   ]);
-  _package.completeInit(seqHelper);
+  _package.completeInit(helmHelper);
 }
 
 //name: Oligo Toolkit
@@ -302,5 +303,5 @@ export async function ptEnumeratorChemApp(): Promise<void> {
 export function applyNotationProviderForCyclized(col: DG.Column<string>, separator: string) {
   col.meta.units = NOTATION.CUSTOM;
   col.tags[PolyToolTags.dataRole] = 'template';
-  col.temp[SeqTemps.notationProvider] = new CyclizedNotationProvider(separator, _package.seqHelper);
+  col.temp[SeqTemps.notationProvider] = new CyclizedNotationProvider(separator, _package.helmHelper);
 }

package/src/polytool/const.ts

@@ -33,6 +33,7 @@ export const PT_WARNING_COLUMN = 'No marcomolecule column chosen!';
 export const PT_UI_GET_HELM = 'Get HELM';
 export const PT_UI_ADD_HELM = 'Add HELM column';
 export const PT_UI_USE_CHIRALITY = 'Chirality engine';
+export const PT_UI_HIGHLIGHT_MONOMERS = 'Highlight monomers';
 export const PT_UI_DIALOG_CONVERSION = 'Poly Tool Conversion';
 export const PT_UI_DIALOG_UNRULE = 'Poly Tool Unrule';
 export const PT_UI_DIALOG_ENUMERATION = 'Poly Tool Enumeration';